Mr. BIPS, let me point you in the right direction...
Sub(s): Sundown SA-12 [Sundown SA-12]
Sub and Speaker amp: [Hifonics Zeus ZXi60.4+1K 5-Channel]
Speakers: DD CS 6.5's all around, make mounting plates for 6.5's to fit in the rear [Digital Designs CS 6.5]
So you're looking at $200 shipped for the sub, $360 shipped for the amp, and about $175 per pair of speakers (call DD for prices). That's $735 for all the main equipment.
You'll also need wiring. I suggest you go with a 1/0ga wiring kit from Knukonceptz [Knukonceptz KCA 1/0ga Amp Installation Kit]. You will also want some extra power wire for the Big 3 Mod (search on google if you are unsure what that is), So just measure the lengths and buy a little more than what you measured here [Knukonceptz KCA 1/0ga Red]
You shouldn't need more than Big 3 and one run of 1/0ga for that kind of power in your car. To be safe, you can always add an extra battery.
Find a good box builder on this site to build you a proper enclosure. Ram Designs, Pro Rabbit, Bassman3, there are a ton of good choices here. I would imagine $250 for a custom box.
So another $60 for the install kit, let's just estimate 15 extra feet of 1/0ga for $30, and $250 for a box. Add that $340 to the previous total of $735 and you get $1075. Spend the rest of the money on the install. Do what you can first, like cut the appropriate lengths of wire, properly mount the sub and wire it in the box, etc. Whatever you feel comfortable doing will save you more money than you think. I don't see why the install should cost more than $1k. You'll be left with a $2k system that will eat that $2800 JL system for lunch!